BILS Proteomics Data Storage Documentation

Here is an overview of what can be installed locally in the proteomics groups. A presentation with a description of the system is found here . Documents with detailed installation and user instructions can be found in the Repository.

Upload computer

Recommended OS for this computer is Ubuntu Server x64, latest version with long term support.

File conversion computer

Should be running Windows 7 or Windows XP. It is also be possible to configure a Windows machine running in Virtual Box on the Linux machine used for file upload.

Proteios configuration

Typically the computer used for upload is also configured with a Proteios installation. It will be the access point to files on Swestore for lab users.

To allow Proteios to use files on Swestore, some configuration needs to be done. The application will need to be configured to use a certificate when accessing files over https, and also it needs to be configured to trust the Swestore server certificates. This is done by setting some Java properties or specifying the properties in the file connection.properties.
Detailed instructions can be found here: http://www.proteios.org/trac/wiki/HttpsRemoteFiles

If Proteios is going to be used for proteomics data analysis, it should be configured to use search engines and feature detection tools:

X!Tandem configuration

If the Proteios server is going to be used for proteomics data analysis it can be installed with an X!tandem server as well. X!tandem can then be used for MS/MS spectrum identification using peptide fragment fingerprinting (PFF).

Mascot configuration

If the lab has a Mascot server, Proteios can be configured to use it for peptide and protein identification using MS and MS/MS.

msInspect / openMS / Dinosaur configuration

If Proteios is going to be used for label free quantification, msInspect, OpenMS and or Dinosaur should also be installed, as these are used for feature detection.